Yesterday, President Obama said he wanted to extend FBI director Bob Mueller’s term for another two years, on top of the 10 Mueller has already served. It’s not only the first time since Hoover that a Bureau director has been asked to stay on. It makes Mueller the only major public official to have kept his job through the entire “War on Terror” era.

Mueller remains largely unknown to the general public. He doesn’t give many interviews to the press, and even some of the people who have worked with him for years say they don’t know him particularly well.

Washingtonian magazine editor Garret Graff is the exception. He has interviewed Mueller at least a half-dozen times, and spent more than a thousand hours speaking to the director, his top aides and 180 current and former officials at the FBI, White House, Justice Department, CIA, NYPD and the Pentagon. These interviews form the heart of Graff’s new book, The Threat Matrix: The FBI at War in the Age of Global Terror.

We talked to Graff about the director’s longevity, Osama bin Laden’s thumb drives, the Bureau’s allergy to technology and the lamest ultimatum by a wannabe terrorist ever.

Wired.com: How has Mueller been able to hang on?

Garrett Graff: Mueller last year became the longest-serving FBI director since J. Edgar Hoover himself and, with this proposed extension by President Obama, will clearly be the most influential director since, as well. There have been five FBI directors since Hoover but Mueller was set to be the first to reach the full 10-year term limit — two directors quit early, one was fired and one was appointed director of the CIA.

What’s particularly impressive about Mueller’s accomplishment is that the job has never been harder than it is today — it’s 24/7 in a way that the job never was under Mueller’s predecessors, with enormous pressures from both U.S. security threats and geopolitical pressures overseas.

I think this is going to be a Cal Ripken-like record, one that we’ve never seen before in modern history and one we’re unlikely to ever see again. Mueller just happened to have a unique constitution — an enormous reserve of physical stamina, the right set of political skills for an apolitical job, and the right mix of management skills necessary to lead and transform an agency in the midst of tremendous pressure.

Wired.com: News reports say that the FBI is part of the team that’s scouring the discs and drives taken from the bin Laden raid. Any insight on what the agents are doing, specifically?

Two FBI agents from the Charlotte Field Office pose before a makeshift sign during their winter deployment to Afghanistan, just some of the hundreds of FBI agents who have worked in war zones since 2001.

Graff: While the bin Laden operation was mostly led by the SEALs and the CIA, the FBI was very much involved in the planning, helping to train the SEALs about how to gather evidence at the scene and ensure the collection of valuable intelligence. Much of that intelligence — the flash drives, documents and so on — is now being worked on by the FBI forensics and laboratory teams (along with other agencies).

The Bureau really pushed the SEALs to preserve forensic evidence like fingerprints on the evidence they collected at the Abbottabad compound so that the FBI lab officials could track every possible lead. The effort to process that information since has been a joint exercise by the FBI, CIA, NSA and Pentagon.

The combat-intelligence role has been one the Bureau has played since the fall of 2001, going into Afghanistan and later Iraq to help gather intelligence, process raid sites for evidence and leads, and conduct interrogations. The first FBI agents in Afghanistan, who went to Kandahar after the invasion in 2001, worked with U.S. special forces to teach them how to treat raid sites as crime scenes with an eye toward gathering what the FBI calls “pocket litter,” the random documents and personal property that was lying around.

Wired.com: Mueller became FBI director just a few days before 9/11. Was this the job he thought he was walking into?

Graff: Mueller actually thought he was showing up to fix the computers. Under his predecessor, Louis Freeh, the Bureau had neglected its IT infrastructure — Freeh himself didn’t like computers — and Mueller’s big challenge was supposed to be fixing that.

Mueller’s a bit of a closet geek — he got onto cybercrime threats very early in his career, launching the Justice Department’s first cyber team, helping to build the computer system used by U.S. Attorneys nationwide, and he’s always quick to purchase the latest gadget — but he came into the job on September 4, 2001, with little knowledge of counterterrorism or the intelligence worlds. I tell the story in the book of how coincidentally he was sitting on the morning of Tuesday, September 11, 2001, in one of his first briefings on al-Qaida when the Trade Centers were attacked.

The irony of just how much Mueller has changed the Bureau in the last decade, overseeing a huge transition toward more intelligence-driven, threat-based cases, is that the Mueller of 2001 would likely not be considered capable of replacing the Mueller of 2011.

Wired.com: Two FBI squads spent years chasing al-Qaida. Yet, after 9/11, Mueller turned the investigation over to a whole different squad. How come?

Graff: There was a feeling — quite wrong, I believe — that because the 9/11 attacks occurred, the FBI teams in New York who had been chasing bin Laden’s organization had failed. Mueller chose to move the al-Qaida investigation from New York to Washington and turn the investigation over to a different squad; most of those key agents from the al-Qaida squads, who at that point had spent years chasing bin Laden and made some key arrests and gathered some critical intelligence on the organization, were sidelined.

Still today, not one of the eight heads of counterterrorism who have served over the last decade had worked al-Qaida before 9/11.

Hours after he tried to flee the country, Times Square bomber Faisal Shahzad’s car was searched by FBI evidence technicians in an empty hangar at JFK Airport.

Wired.com: You write that Mueller was key to Dick Cheney’s agenda to radically expand executive power after 9/11 — and to largely control the levers of the security state personally. How?

Graff: Mueller served a tour in Vietnam and won a Purple Heart and Bronze Star with valor leading a Marine platoon there. He’s a good Marine — he keeps his head down, keeps a low profile in the media, and doesn’t stray outside his lane, responsibility-wise. It’s one of the political skills that has kept him in the job as director for so long.

Vice President Cheney radically shaped the nation’s response to 9/11, putting the CIA much more at the fore of the response than it had been traditionally, and greatly expanding the military’s role through programs like Guantanamo and enhanced interrogations. The FBI, which until 9/11 had really been the lead agency in responding to terrorism attacks like Pan Am 103 and the East Africa embassy bombings, was sidelined in some key respects.

Mueller, while he has his own firmly developed sense of Constitutional rights and protections, didn’t see his role as advocating for specific policies — he saw his role as executing the agenda presented by the president and vice president. Even though he disagreed with many of the decisions made in the wake of 9/11, he protested remarkably little.

Wired.com: After 9/11, you write, the federal government lost all sense of proportion when it came to terror. Any potential whisper of terrorism got put on the “threat matrix,” the list of potential plots forwarded to the White House. (My personal favorite: the e-mail that read, “Dear America, I will attack you if you don’t pay me 999999999999999999999999999999999999999999 dollars. MUHAHAHA.”) Tell
us how the threat matrix drove the agenda in those years — and how long it took for sanity to return.

Graff: The name of the book, The Threat Matrix, comes from the document that the FBI and the CIA developed after 9/11 to track the the unfolding terrorism plots. Each morning, CIA director George Tenet, FBI director Mueller, President Bush, Vice President Cheney and other national security officials, spent an hour going over that document — it was a spreadsheet, actually, that many days stretched to 15 to 20 pages, outlining every piece of intelligence and unfolding plot gathered by the U.S. government in the previous 24 hours.

The problem with the document, though, was that everyone wanted to share everything — so most of the stuff listed in the threat matrix was bunk at best, specious rumors, half-baked analysis and half-true exaggerations. The team in the Oval Office, though, didn’t know that, so they had to treat everything as a serious threat — the document really numbed them and made it hard to make smart decisions about how real and expansive the terrorist threat was after 9/11.

The best example of this is about a month after 9/11, a report came in on the threat matrix that a nuclear weapon was on board a train bound for Pittsburgh, set to be detonated within 24 hours. That obviously spun up the government and put people into panic mode. It took a couple of days to run down that the intelligence actually originated from a misheard conversation in a men’s bathroom in the Ukraine, there was no basis in reality at all. For weeks, President Bush teased the men briefing him, “Is this another Ukrainian urinal incident?”

Special agents Fred Bradford and Richard Kolko raised an FBI flag on top of the Bureau’s first Iraq headquarters, on the outskirts of Baghdad International Airport, in April 2003.

Wired.com: What steps did Mueller take to reorient the FBI around counterterror?

Graff: The biggest shift under Mueller is that counterterrorism has gone from one of the top priorities to the top priority. That’s meant they’ve reshuffled thousands of agents from other tasks.

It’s also meant that they’ve really accelerated a push overseas that began in the 1990s. The FBI, which originally was designed as a domestic agency, today operates in about 80 countries overseas and has hundreds of agents deployed to places like Afghanistan, Iraq, Pakistan and other global hotspots. Agents are in Thailand working organized crime cases, in Africa doing kidnapping cases, Latin America doing drugs and gangs, and in Eastern Europe doing cybercrime cases.

The FBI actually last month conducted its first raid on the ground in Somalia, going in to capture a pirate ringleader and bring him back to the U.S. to stand trial. J. Edgar Hoover really wouldn’t recognize much of the work that Mueller’s FBI does today.

Wired.com: When Mueller took the helm of the FBI, its computer systems were woefully out of date. Have they gotten any better, relatively speaking? Does the Bureau have an electronic case-record system yet, for instance?Graff: The FBI’s computer upgrade has been by most accounts the biggest failure of Mueller’s tenure — it went wildly off track in the years after 9/11, running hundreds of millions of dollars over budget and years behind schedule. Only in the last couple of years has it gotten on track and begun delivering real value to agents.

It’s come a long way since 2001 — I tell the story in the book of how in the summer of 2001, FBI agents in San Francisco had no way to transfer an al-Qaida’s suspect e-mail securely to agents in New York; they had to save the e-mail to a floppy disc and fly commercially to LaGuardia to hand-deliver the disc. But the FBI still isn’t where many people had hoped they’d be.

While agents now can do things like share information better, access the internet at their desks, and use BlackBerrys — you might laugh but many of these innovations were years in coming — the case-management system is really the last puzzle piece and that is scheduled to be completed by next year. One good argument for extending Mueller’s term is the chance for him to see that full process through and not change horses midstream.

I believe though that the computer system is just one part of the big picture: I still think that the FBI is underinvesting in cyberthreats right now in the same way that it underinvested in counterterrorism in the 1990s.

Wired.com: What were the downsides of turning the FBI into more of a counterterror shop? What was lost, as a result?

Graff: The reassignment of so many agents to counterterrorism and the re-prioritization on national security hasn’t been without cost. We haven’t pumped new staff into the FBI at the rate that we have in other homeland security agencies since 9/11, which means that many of the new CT agents have been pulled from the traditional criminal divisions of the FBI — squads that investigated things like bank robberies, fraud, white collar crime and particularly drug cases.

In many of those areas, prosecutions have dropped by 40, 50, and even 60 percent. Mueller, for instance, pulled 2,000 agents off the southern border who had been working big drug cases — and that reassignment actually tracks pretty closely to the tremendous rise of violence in the Mexican drug world over the last decade.

I think part of President Obama’s decision to extend Mueller’s term by two years is to give him a chance to continue the rebuilding of the criminal division, a process that Mueller began about two years ago. He’s got one of his most favored executives, TJ Harrington, heading that process now, trying to bring some of the same evolution in thinking that they’ve applied to counterterrorism — focusing more on threats and intelligence — to the criminal investigation process.

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